15-68304789-T-C

Variant names:

• chr15-68304789-T-C
• rs7174755
• NM_001004439.2:c.3382-904A>G

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The NM_001004439.2(ITGA11):​c.3382-904A>G variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.35 in 152,038 control chromosomes in the GnomAD database, including 10,051 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.35 (10051 hom., cov: 32)
• Consequence: ITGA11 NM_001004439.2 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.45
• Publications: 24 publications found

Genes affected

ITGA11 (HGNC:6136): (integrin subunit alpha 11) This gene encodes an alpha integrin. Integrins are heterodimeric integral membrane proteins composed of an alpha chain and a beta chain. This protein contains an I domain, is expressed in muscle tissue, dimerizes with beta 1 integrin in vitro, and appears to bind collagen in this form. Therefore, the protein may be involved in attaching muscle tissue to the extracellular matrix. Alternative transcriptional splice variants have been found for this gene, but their biological validity is not determined. [provided by RefSeq, Jul 2008]

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.89).
• BA1: GnomAd4 highest subpopulation (AFR) allele frequency at 95% confidence interval = 0.451 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt
ITGA11	NM_001004439.2	c.3382-904A>G		intron_variant	Intron 28 of 29	ENST00000315757.9	NP_001004439.1
ITGA11	XM_011521363.3	c.3175-904A>G		intron_variant	Intron 26 of 27		XP_011519665.1
ITGA11	XM_005254228.4	c.3076-904A>G		intron_variant	Intron 26 of 27		XP_005254285.1

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt
ITGA11	ENST00000315757.9	c.3382-904A>G		intron_variant	Intron 28 of 29	1	NM_001004439.2	ENSP00000327290.7
ITGA11	ENST00000423218.6	c.3385-904A>G		intron_variant	Intron 28 of 29	2		ENSP00000403392.2

Frequencies

GnomAD3 genomes AF: 0.350 AC: 53128 AN: 151920 Hom.: 10041 Cov.: 32

Gnomad AFR AF: 0.457

Gnomad AMI AF: 0.330

Gnomad AMR AF: 0.292

Gnomad ASJ AF: 0.359

Gnomad EAS AF: 0.0351

Gnomad SAS AF: 0.129

Gnomad FIN AF: 0.306

Gnomad MID AF: 0.351

Gnomad NFE AF: 0.343

Gnomad OTH AF: 0.376

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.350 AC: 53179 AN: 152038 Hom.: 10051 Cov.: 32 AF XY: 0.341 AC XY: 25355 AN XY: 74318

African (AFR) AF: 0.457 AC: 18935 AN: 41450

American (AMR) AF: 0.292 AC: 4469 AN: 15280

Ashkenazi Jewish (ASJ) AF: 0.359 AC: 1246 AN: 3472

East Asian (EAS) AF: 0.0346 AC: 179 AN: 5176

South Asian (SAS) AF: 0.129 AC: 623 AN: 4824

European-Finnish (FIN) AF: 0.306 AC: 3237 AN: 10570

Middle Eastern (MID) AF: 0.340 AC: 100 AN: 294

European-Non Finnish (NFE) AF: 0.343 AC: 23301 AN: 67946

Other (OTH) AF: 0.373 AC: 788 AN: 2114

Alfa AF: 0.344 Hom.: 29591

Bravo AF: 0.356

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.89
CADD	Benign	0.57
DANN	Benign	0.40
PhyloP100		-1.4
Mutation Taster		=100/0	polymorphism (auto)

Splicing

Name	Calibrated prediction	Score	Prediction
SpliceAI score (max)		0.010		Details are displayed if max score is > 0.2

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Other links and lift over

dbSNP: rs7174755; hg19: chr15-68597127;